arXiv subjects

Rickmer Braren

Publications and source records attributed to Rickmer Braren.

At least 19 recordsLinked to original sources

arXiv2026

NOAH: Learning the Full Patient Journey. A Longitudinal Multimodal Time-Aware Model for Representation and Forecasting

The digitization of healthcare has generated vast, longitudinal, and multimodal patient records over a lifetime, yet fully exploiting these data to represent and predict patient state trajectories remains a critical challenge. Current AI models often struggle to capture the complex, irregular temporal dynamics and inherent stochasticity of real-world multimodal patient data. Existing AI approaches for modeling longitudinal patient records are predominantly discriminative, limited to a few modalities, constrained by closed categorical vocabularies, treating time as a monotonic inductive bias, or they are limited in forecasting future patient states. We introduce NOAH, a time-aware, task-agnostic, generative transformer model representing and forecasting the full multimodal patient journey. NOAH features a novel bidirectional time integration and a variational latent space to capture the continuous evolution of patient states and the stochasticity of clinical trajectories. Built from over 559 million clinical events from 431,000 hospital visits of 299,000 patients across the MIMIC dataset family, NOAH natively processes medical images, time-series and numeric signals, categorical events, as well as structured and unstructured clinical records. NOAH is the first truly holistic generative model in its field, enabling autoregressive forecasting with optional time control, zero-shot classification, and counterfactual intervention simulation. It generates highly informative and predictive patient state representations that demonstrate strong performance in probing for clinical outcomes, 15 ICD chapters, and 29 comorbidities, as well as in time-to-event prediction. Seamlessly handling diverse modalities and complex temporal dynamics, NOAH provides a versatile, task-agnostic, scalable foundation for intelligent predictive systems in personalized clinical care and digital medicine.

cs.LG↗

arXiv2026

It depends: Incorporating correlations for joint aleatoric and epistemic uncertainties of high-dimensional output spaces

Uncertainty Quantification (UQ) plays a vital role in enhancing the reliability of deep learning model predictions, especially in scenarios with high-dimensional output spaces. This paper addresses the dual nature of uncertainty -- aleatoric and epistemic -- focusing on their joint integration in high-dimensional regression tasks. For example, in applications like medical image segmentation or restoration, aleatoric uncertainty captures inherent data noise, while epistemic uncertainty quantifies the model's confidence in unfamiliar conditions. Modeling both jointly enables more reliable predictions by reflecting both unavoidable variability and knowledge gaps, whereas modeling only one limits transparency and robustness. We propose a novel approach that approximates the resulting joint uncertainty using a low-rank plus diagonal covariance structure, capturing essential output correlations while avoiding the computational burdens of full covariance matrices. Unlike prior work, our method explicitly combines aleatoric and epistemic uncertainties into a unified second-order distribution that supports robust downstream analyses like sampling and log-likelihood evaluation. We further introduce stabilization strategies for efficient training and inference, achieving superior UQ in the tasks of image inpainting, colorization, optical flow, and depth estimation.

cs.LG↗

arXiv2026

Big, Bright, or Invisible: A Frozen-Feature Benchmark of 3D CT Foundation Models

Routine CT interpretation is inherently comprehensive, capturing incidental findings across the entire scan volume. 3D CT foundation models could assist this process by providing generalizable representations of anatomy and pathology. To evaluate their diagnostic breadth, we benchmark ten frozen CT encoders across three cohorts of thoracic CT scans, including an unseen internal clinical dataset, using $k$-nearest neighbors, zero-shot prompting, and linear probing. We find no universal state-of-the-art, with rankings fluctuating significantly depending on the evaluation context. While models combining fine-grained image tokenization with vision-language alignment generally perform best, a lightweight supervised encoder remains highly competitive, demonstrating that explicit labels can effectively substitute for scale. Crucially, rather than model architecture, we observe that the primary determinant of performance is a physical bottleneck: a finding's detectability scales with its contrast against surrounding tissue and its spatial extent. Through controlled within-organ comparisons, we empirically demonstrate that widespread or high-contrast abnormalities, such as devices and effusions, are reliably recovered. Conversely, small, low-contrast focal lesions remain a persistent challenge across all evaluated encoders. We attribute this to the inherent limitations of globally pooled embeddings, suggesting that accurately representing small, low-contrast structures will require region- or lesion-level pretraining.

cs.CV↗

arXiv2026

MIA: A Visual Analytics System for Multimodal Spectral Imaging Data

Hyperspectral bioimaging techniques such as infrared (IR) microscopy and laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) produce high-dimensional, spatially resolved datasets that require sophisticated analysis to reveal chemically and anatomically meaningful structures. Existing software solutions are typically modality-specific and cover only parts of the analytical workflow, forcing researchers to transfer data across multiple tools and manually reconcile results. We present MIA (Multiscale Image Analysis), a modality-agnostic visual analysis environment that integrates the full exploratory workflow -- from spectral preprocessing and dimensionality reduction to interactive segmentation and spectral similarity analysis -- within a single, tightly coupled interface. MIA supports hierarchical and landmark-based embeddings to handle datasets of varying scale and complexity, interactive and automatic segmentation with a shared state across all linked views, and multimodal analysis of co-registered datasets from different instruments. We demonstrate the effectiveness of MIA through three use cases drawn from real analytical chemistry workflows: (1) the recovery of biologically meaningful tissue compartments through derivative preprocessing and hierarchical embedding, (2) pigment identification via spectral similarity search with spatial overview, and (3) multimodal tissue characterization combining molecular IR and elemental LA-ICP-MS data. Qualitative feedback from domain expert collaborators confirms that MIA reduces the need for tool-switching and supports analytical insights that are difficult to obtain with existing software.

cs.HC↗

arXiv2026

Survival In-Context: Amortized Bayesian Survival Analysis via Prior-Fitted Networks

Survival analysis is crucial for many medical applications, but remains challenging for modern machine learning due to limited data, censoring, and the heterogeneity of tabular covariates. While the prior-fitted paradigm, which relies on pretraining models on large collections of synthetic datasets, has recently facilitated tabular foundation models for classification and regression, its suitability for time-to-event modeling remains unclear. We propose a flexible survival data generation framework that defines a rich survival prior with explicit control over covariates and time-event distributions. Building on this prior, we introduce Survival In-Context (SIC), a prior-fitted in-context learning model for survival analysis that is pretrained exclusively on synthetic data. SIC is trained to approximate Bayesian posterior predictive inference under the synthetic survival prior, enabling individualized survival prediction in a single forward pass, requiring no task-specific training or hyperparameter tuning. Across a broad evaluation on real-world survival datasets, SIC achieves competitive or superior performance compared to classical and deep survival models, particularly in small and medium-sized data regimes, highlighting the promise of a prior-fitted paradigm for survival analysis. The code and pretrained models will be made available upon publication.

cs.LG↗

arXiv2026

Calibrated Confidence Expression for Radiology Report Generation

Safe deployment of Large Vision-Language Models (LVLMs) in radiology report generation requires not only accurate predictions but also clinically interpretable indicators of when outputs should be thoroughly reviewed, enabling selective radiologist verification and reducing the risk of hallucinated findings influencing clinical decisions. One intuitive approach to this is verbalized confidence, where the model explicitly states its certainty. However, current state-of-the-art language models are often overconfident, and research on calibration in multimodal settings such as radiology report generation is limited. To address this gap, we introduce ConRad (Confidence Calibration for Radiology Reports), a reinforcement learning framework for fine-tuning medical LVLMs to produce calibrated verbalized confidence estimates alongside radiology reports. We study two settings: a single report-level confidence score and a sentence-level variant assigning a confidence to each claim. Both are trained using the GRPO algorithm with reward functions based on the logarithmic scoring rule, which incentivizes truthful self-assessment by penalizing miscalibration and guarantees optimal calibration under reward maximization. Experimentally, ConRad substantially improves calibration and outperforms competing methods. In a clinical evaluation we show that ConRad's report level scores are well aligned with clinicians' judgment. By highlighting full reports or low-confidence statements for targeted review, ConRad can support safer clinical integration of AI-assistance for report generation.

cs.CL↗

arXiv2025

MedDIFT: Multi-Scale Diffusion-Based Correspondence in 3D Medical Imaging

Accurate spatial correspondence between medical images is essential for longitudinal analysis, lesion tracking, and image-guided interventions. Medical image registration methods rely on local intensity-based similarity measures, which fail to capture global semantic structure and often yield mismatches in low-contrast or anatomically variable regions. Recent advances in diffusion models suggest that their intermediate representations encode rich geometric and semantic information. We present MedDIFT, a training-free 3D correspondence framework that leverages multi-scale features from a pretrained latent medical diffusion model as voxel descriptors. MedDIFT fuses diffusion activations into rich voxel-wise descriptors and matches them via cosine similarity, with an optional local-search prior. On a publicly available lung CT dataset, MedDIFT shows promising capability in identifying anatomical correspondence without requiring any task-specific model training. Ablation experiments confirm that multi-level feature fusion and modest diffusion noise improve performance. Code is available online.

cs.CV↗

arXiv2025

LungEvaty: A Scalable, Open-Source Transformer-based Deep Learning Model for Lung Cancer Risk Prediction in LDCT Screening

Lung cancer risk estimation is gaining increasing importance as more countries introduce population-wide screening programs using low-dose CT (LDCT). As imaging volumes grow, scalable methods that can process entire lung volumes efficiently are essential to tap into the full potential of these large screening datasets. Existing approaches either over-rely on pixel-level annotations, limiting scalability, or analyze the lung in fragments, weakening performance. We present LungEvaty, a fully transformer-based framework for predicting 1-6 year lung cancer risk from a single LDCT scan. The model operates on whole-lung inputs, learning directly from large-scale screening data to capture comprehensive anatomical and pathological cues relevant for malignancy risk. Using only imaging data and no region supervision, LungEvaty matches state-of-the-art performance, refinable by an optional Anatomically Informed Attention Guidance (AIAG) loss that encourages anatomically focused attention. In total, LungEvaty was trained on more than 90,000 CT scans, including over 28,000 for fine-tuning and 6,000 for evaluation. The framework offers a simple, data-efficient, and fully open-source solution that provides an extensible foundation for future research in longitudinal and multimodal lung cancer risk prediction.

cs.CV↗

arXiv2025

Whole-body Representation Learning For Competing Preclinical Disease Risk Assessment

Reliable preclinical disease risk assessment is essential to move public healthcare from reactive treatment to proactive identification and prevention. However, image-based risk prediction algorithms often consider one condition at a time and depend on hand-crafted features obtained through segmentation tools. We propose a whole-body self-supervised representation learning method for the preclinical disease risk assessment under a competing risk modeling. This approach outperforms whole-body radiomics in multiple diseases, including cardiovascular disease (CVD), type 2 diabetes (T2D), chronic obstructive pulmonary disease (COPD), and chronic kidney disease (CKD). Simulating a preclinical screening scenario and subsequently combining with cardiac MRI, it sharpens further the prediction for CVD subgroups: ischemic heart disease (IHD), hypertensive diseases (HD), and stroke. The results indicate the translational potential of whole-body representations as a standalone screening modality and as part of a multi-modal framework within clinical workflows for early personalized risk stratification. The code is available at https://github.com/yayapa/WBRLforCR/

cs.CV↗

arXiv2025

On Arbitrary Predictions from Equally Valid Models

Model multiplicity refers to the existence of multiple machine learning models that describe the data equally well but may produce different predictions on individual samples. In medicine, these models can admit conflicting predictions for the same patient -- a risk that is poorly understood and insufficiently addressed. In this study, we empirically analyze the extent, drivers, and ramifications of predictive multiplicity across diverse medical tasks and model architectures, and show that even small ensembles can mitigate/eliminate predictive multiplicity in practice. Our analysis reveals that (1) standard validation metrics fail to identify a uniquely optimal model and (2) a substantial amount of predictions hinges on arbitrary choices made during model development. Using multiple models instead of a single model reveals instances where predictions differ across equally plausible models -- highlighting patients that would receive arbitrary diagnoses if any single model were used. In contrast, (3) a small ensemble paired with an abstention strategy can effectively mitigate measurable predictive multiplicity in practice; predictions with high inter-model consensus may thus be amenable to automated classification. While accuracy is not a principled antidote to predictive multiplicity, we find that (4) higher accuracy achieved through increased model capacity reduces predictive multiplicity. Our findings underscore the clinical importance of accounting for model multiplicity and advocate for ensemble-based strategies to improve diagnostic reliability. In cases where models fail to reach sufficient consensus, we recommend deferring decisions to expert review.

cs.LG↗

arXiv2025

Parametric shape models for vessels learned from segmentations via differentiable voxelization

Vessels are complex structures in the body that have been studied extensively in multiple representations. While voxelization is the most common of them, meshes and parametric models are critical in various applications due to their desirable properties. However, these representations are typically extracted through segmentations and used disjointly from each other. We propose a framework that joins the three representations under differentiable transformations. By leveraging differentiable voxelization, we automatically extract a parametric shape model of the vessels through shape-to-segmentation fitting, where we learn shape parameters from segmentations without the explicit need for ground-truth shape parameters. The vessel is parametrized as centerlines and radii using cubic B-splines, ensuring smoothness and continuity by construction. Meshes are differentiably extracted from the learned shape parameters, resulting in high-fidelity meshes that can be manipulated post-fit. Our method can accurately capture the geometry of complex vessels, as demonstrated by the volumetric fits in experiments on aortas, aneurysms, and brain vessels.

cs.CV↗

arXiv2025

Temporal Neural Cellular Automata: Application to modeling of contrast enhancement in breast MRI

Synthetic contrast enhancement offers fast image acquisition and eliminates the need for intravenous injection of contrast agent. This is particularly beneficial for breast imaging, where long acquisition times and high cost are significantly limiting the applicability of magnetic resonance imaging (MRI) as a widespread screening modality. Recent studies have demonstrated the feasibility of synthetic contrast generation. However, current state-of-the-art (SOTA) methods lack sufficient measures for consistent temporal evolution. Neural cellular automata (NCA) offer a robust and lightweight architecture to model evolving patterns between neighboring cells or pixels. In this work we introduce TeNCA (Temporal Neural Cellular Automata), which extends and further refines NCAs to effectively model temporally sparse, non-uniformly sampled imaging data. To achieve this, we advance the training strategy by enabling adaptive loss computation and define the iterative nature of the method to resemble a physical progression in time. This conditions the model to learn a physiologically plausible evolution of contrast enhancement. We rigorously train and test TeNCA on a diverse breast MRI dataset and demonstrate its effectiveness, surpassing the performance of existing methods in generation of images that align with ground truth post-contrast sequences.

eess.IV↗

arXiv2025

Automated Thoracolumbar Stump Rib Detection and Analysis in a Large CT Cohort

Thoracolumbar stump ribs are one of the essential indicators of thoracolumbar transitional vertebrae or enumeration anomalies. While some studies manually assess these anomalies and describe the ribs qualitatively, this study aims to automate thoracolumbar stump rib detection and analyze their morphology quantitatively. To this end, we train a high-resolution deep-learning model for rib segmentation and show significant improvements compared to existing models (Dice score 0.997 vs. 0.779, p-value < 0.01). In addition, we use an iterative algorithm and piece-wise linear interpolation to assess the length of the ribs, showing a success rate of 98.2%. When analyzing morphological features, we show that stump ribs articulate more posteriorly at the vertebrae (-19.2 +- 3.8 vs -13.8 +- 2.5, p-value < 0.01), are thinner (260.6 +- 103.4 vs. 563.6 +- 127.1, p-value < 0.01), and are oriented more downwards and sideways within the first centimeters in contrast to full-length ribs. We show that with partially visible ribs, these features can achieve an F1-score of 0.84 in differentiating stump ribs from regular ones. We publish the model weights and masks for public use.

cs.CV↗

arXiv2025

Enhanced Diagnostic Fidelity in Pathology Whole Slide Image Compression via Deep Learning

Accurate diagnosis of disease often depends on the exhaustive examination of Whole Slide Images (WSI) at microscopic resolution. Efficient handling of these data-intensive images requires lossy compression techniques. This paper investigates the limitations of the widely-used JPEG algorithm, the current clinical standard, and reveals severe image artifacts impacting diagnostic fidelity. To overcome these challenges, we introduce a novel deep-learning (DL)-based compression method tailored for pathology images. By enforcing feature similarity of deep features between the original and compressed images, our approach achieves superior Peak Signal-to-Noise Ratio (PSNR), Multi-Scale Structural Similarity Index (MS-SSIM), and Learned Perceptual Image Patch Similarity (LPIPS) scores compared to JPEG-XL, Webp, and other DL compression methods.

eess.IV↗

arXiv2024

Self-Supervised Radiograph Anatomical Region Classification -- How Clean Is Your Real-World Data?

Modern deep learning-based clinical imaging workflows rely on accurate labels of the examined anatomical region. Knowing the anatomical region is required to select applicable downstream models and to effectively generate cohorts of high quality data for future medical and machine learning research efforts. However, this information may not be available in externally sourced data or generally contain data entry errors. To address this problem, we show the effectiveness of self-supervised methods such as SimCLR and BYOL as well as supervised contrastive deep learning methods in assigning one of 14 anatomical region classes in our in-house dataset of 48,434 skeletal radiographs. We achieve a strong linear evaluation accuracy of 96.6% with a single model and 97.7% using an ensemble approach. Furthermore, only a few labeled instances (1% of the training set) suffice to achieve an accuracy of 92.2%, enabling usage in low-label and thus low-resource scenarios. Our model can be used to correct data entry mistakes: a follow-up analysis of the test set errors of our best-performing single model by an expert radiologist identified 35% incorrect labels and 11% out-of-domain images. When accounted for, the radiograph anatomical region labelling performance increased -- without and with an ensemble, respectively -- to a theoretical accuracy of 98.0% and 98.8%.

cs.CV↗

arXiv2024

Unlocking the Potential of Digital Pathology: Novel Baselines for Compression

Digital pathology offers a groundbreaking opportunity to transform clinical practice in histopathological image analysis, yet faces a significant hurdle: the substantial file sizes of pathological Whole Slide Images (WSI). While current digital pathology solutions rely on lossy JPEG compression to address this issue, lossy compression can introduce color and texture disparities, potentially impacting clinical decision-making. While prior research addresses perceptual image quality and downstream performance independently of each other, we jointly evaluate compression schemes for perceptual and downstream task quality on four different datasets. In addition, we collect an initially uncompressed dataset for an unbiased perceptual evaluation of compression schemes. Our results show that deep learning models fine-tuned for perceptual quality outperform conventional compression schemes like JPEG-XL or WebP for further compression of WSI. However, they exhibit a significant bias towards the compression artifacts present in the training data and struggle to generalize across various compression schemes. We introduce a novel evaluation metric based on feature similarity between original files and compressed files that aligns very well with the actual downstream performance on the compressed WSI. Our metric allows for a general and standardized evaluation of lossy compression schemes and mitigates the requirement to independently assess different downstream tasks. Our study provides novel insights for the assessment of lossy compression schemes for WSI and encourages a unified evaluation of lossy compression schemes to accelerate the clinical uptake of digital pathology.

eess.IV↗

arXiv2024

General Vision Encoder Features as Guidance in Medical Image Registration

General vision encoders like DINOv2 and SAM have recently transformed computer vision. Even though they are trained on natural images, such encoder models have excelled in medical imaging, e.g., in classification, segmentation, and registration. However, no in-depth comparison of different state-of-the-art general vision encoders for medical registration is available. In this work, we investigate how well general vision encoder features can be used in the dissimilarity metrics for medical image registration. We explore two encoders that were trained on natural images as well as one that was fine-tuned on medical data. We apply the features within the well-established B-spline FFD registration framework. In extensive experiments on cardiac cine MRI data, we find that using features as additional guidance for conventional metrics improves the registration quality. The code is available at github.com/compai-lab/2024-miccai-koegl.

cs.CV↗

arXiv2024

Data-Driven Tissue- and Subject-Specific Elastic Regularization for Medical Image Registration

Physics-inspired regularization is desired for intra-patient image registration since it can effectively capture the biomechanical characteristics of anatomical structures. However, a major challenge lies in the reliance on physical parameters: Parameter estimations vary widely across the literature, and the physical properties themselves are inherently subject-specific. In this work, we introduce a novel data-driven method that leverages hypernetworks to learn the tissue-dependent elasticity parameters of an elastic regularizer. Notably, our approach facilitates the estimation of patient-specific parameters without the need to retrain the network. We evaluate our method on three publicly available 2D and 3D lung CT and cardiac MR datasets. We find that with our proposed subject-specific tissue-dependent regularization, a higher registration quality is achieved across all datasets compared to using a global regularizer. The code is available at https://github.com/compai-lab/2024-miccai-reithmeir.

cs.CV↗